49ers’ Mac Jones, who played for Saban and Belichick, turns to Kyle Shanahan for help

SANTA CLARA — It wasn’t the greatest of practice sessions Wednesday for 49ers quarterback Mac Jones.

He had a pass intercepted by Derrick Canteen when it appeared he and receiver Russell Gage Jr. were not on the same page. Jones overthrew rookie Jordan Watkins on a post. Had passes broken up over the middle on some 49ers’ bread-and-butter crossing routes.

Jones wasn’t nearly as efficient as starter Brock Purdy, which is understandable.

Just another day in a June no-contact practice where the 49ers’ backup for their $265 million starter is learning the ropes as a valuable insurance policy.  Mick Lombardi, the 49ers’ quarterbacks coach, was in his ear.

“Today was a little bit shaky for me, but that’s how practice goes,” Jones said. “My goal has been, every attempt should be committed to the throw. Mick’s talked to me about that. If it’s supposed to go to that guy, go in there and rip it and live with the result and that’s all you can do. And this playbook is based on footwork, on timing.”

Jones, 26, played in college at Alabama for Nick Saban, one of the best coaches in college football history. He was drafted in the first round by Bill Belichick of New England at No. 15 overall, one of the best coaches in pro football history.

Yet to jump-start his career, Jones turned to Kyle Shanahan, the guy who ultimately rejected the idea of taking Jones in the first round and instead, along with general manager John Lynch, made the regrettable decision to trade up to select Trey Lance.

Jones and Shanahan have only briefly discussed the snub.

“We got in a huge fight,” Jones said in a failed attempt at deadpan humor. “I’m just kidding. We were cool.”

Jones, who finished second in the Heisman Trophy voting to teammate DeVonta Smith in 2020, is taking the Sam Darnold route and hoping it pays similar dividends. Darnold, a former No. 3 overall pick, flamed out in poor situations with the New York Jets and Carolina Panthers and signed on to back up Brock Purdy in 2023.

After looking steady in backup duty with the 49ers, Darnold excelled last season in Minnesota and cashed in to the tune of a three-year deal with $55 million guaranteed with Seattle. Jones, who played with both New England and last season with Jacksonville, came to the 49ers on a two-year deal worth a maximum of $11.5 million to back up Purdy in 2025.

For some reason, backup quarterbacks who make decent money are often disparaged when they should be celebrated. It makes no sense to short-change the most important position in professional sports should the starter go down.

As good as Purdy has been, he hasn’t been made of cast iron. There was an elbow reconstruction following the 2022 season. He missed one game in 2023 and two more last year. And although the 49ers had myriad problems last season, their backup situation with Brandon Allen and Josh Dobbs wasn’t going to pull the team out of their tailspin.

So Shanahan and Co. invested in Jones, much as they sunk money into Jimmy Garoppolo to backup Lance in 2022 and then Darnold in 2023. It gives the 49ers a young quarterback who is looking for a restart.

“When you look at the stats around the league, they’re always in the top five,” Jones said. “I always loved watching what Kyle did throughout the years and to finally get in and learn it, it’s been a little bit challenging, but it’s also a great challenge because it’s something things I’ve done and some things I haven’t done at all.”

Lombardi, who took over for Brian Griese as the quarterbacks coach and was a New England assistant when Jones was a rookie who won 10 games, believes his backup is a rhythm-and-timing passer who should excel in the system.

“In Mac’s four years, he’s won games, he’s really smart, can distribute the football and can play on time and in rhythm,” Lombardi said. “That obviously made him a strong candidate for him to be the backup here behind Brock.”

While it’s not necessary for quarterbacks to be buddy-buddy — it wasn’t the case for Joe Montana and Steve Young or for Young and Jeff Garcia — Jones and Purdy have known each other for some time.

When Purdy got a belated recruited pitch from Alabama as an Arizona high school senior, his host was Jones. The two also worked out in the offseason at Jacksonville with other quarterbacks and receivers.

“We talk about that and how crazy the world works,” Jones said. “His story is so cool to me. Going where he went in the draft, working his butt off and getting what he deserves, that’s something anybody can look at and be like, ‘That’s impressive.’ He will do everything the right way and that’s something that stuck out to me.”

Said Purdy: “We were both young kids heading into college and now we’re on the same team. It’s pretty cool.”

Jones isn’t shying away from the idea that he’s taking the Darnold route.

“Multiple quarterbacks have played in the system really well and that’s the enticing part about it,” Jones said. “I’m going to be my own person and my goal is to be ready when I have to play or if that comes up. All you can do is learn from every rep you get and every rep you don’t get back there watching Brock. I have to continue to build on that.”